Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/summarizecoverage.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 #!/bin/bash |
| jpayne@69 | 2 |
| jpayne@69 | 3 usage(){ |
| jpayne@69 | 4 echo " |
| jpayne@69 | 5 Written by Brian Bushnell |
| jpayne@69 | 6 Last modified April 5, 2020 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Summarizes coverage information from basecov files |
| jpayne@69 | 9 created by pileup.sh. They should be named like |
| jpayne@69 | 10 'sample1_basecov.txt' but other naming styles are fine too. |
| jpayne@69 | 11 |
| jpayne@69 | 12 Usage: summarizecoverage.sh *basecov.txt out=<output file> |
| jpayne@69 | 13 |
| jpayne@69 | 14 Parameters: |
| jpayne@69 | 15 in=<file> 'in=' is not necessary. Any filename used as a |
| jpayne@69 | 16 parameter will be assumed to be an input basecov file. |
| jpayne@69 | 17 out=<file> Write the summary here. Default is stdout. |
| jpayne@69 | 18 reflen=-1 If positive, use this as the total reference length. |
| jpayne@69 | 19 Otherwise, assume basecov files report every ref base. |
| jpayne@69 | 20 |
| jpayne@69 | 21 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 22 " |
| jpayne@69 | 23 } |
| jpayne@69 | 24 |
| jpayne@69 | 25 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 26 pushd . > /dev/null |
| jpayne@69 | 27 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 28 while [ -h "$DIR" ]; do |
| jpayne@69 | 29 cd "$(dirname "$DIR")" |
| jpayne@69 | 30 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 31 done |
| jpayne@69 | 32 cd "$(dirname "$DIR")" |
| jpayne@69 | 33 DIR="$(pwd)/" |
| jpayne@69 | 34 popd > /dev/null |
| jpayne@69 | 35 |
| jpayne@69 | 36 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 37 CP="$DIR""current/" |
| jpayne@69 | 38 |
| jpayne@69 | 39 z="-Xmx200m" |
| jpayne@69 | 40 set=0 |
| jpayne@69 | 41 |
| jpayne@69 | 42 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 43 usage |
| jpayne@69 | 44 exit |
| jpayne@69 | 45 fi |
| jpayne@69 | 46 |
| jpayne@69 | 47 calcXmx () { |
| jpayne@69 | 48 source "$DIR""/calcmem.sh" |
| jpayne@69 | 49 setEnvironment |
| jpayne@69 | 50 parseXmx "$@" |
| jpayne@69 | 51 } |
| jpayne@69 | 52 calcXmx "$@" |
| jpayne@69 | 53 |
| jpayne@69 | 54 summarize() { |
| jpayne@69 | 55 local CMD="java $EA $EOOM $z -cp $CP covid.SummarizeCoverage $@" |
| jpayne@69 | 56 # echo $CMD >&2 |
| jpayne@69 | 57 eval $CMD |
| jpayne@69 | 58 } |
| jpayne@69 | 59 |
| jpayne@69 | 60 summarize "$@" |